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<li class="toctree-l2 current"><a class="current reference internal" href="#">Adaptive QM/MM MD of Fracture in Silicon</a><ul>
<li class="toctree-l3"><a class="reference internal" href="adaptive-qmmm-step0.html">Introduction</a></li>
<li class="toctree-l3"><a class="reference internal" href="adaptive-qmmm-theory.html">Theoretical background</a></li>
<li class="toctree-l3"><a class="reference internal" href="adaptive-qmmm-step1.html">Step 1: Setup of the Silicon model system</a></li>
<li class="toctree-l3"><a class="reference internal" href="adaptive-qmmm-step2.html">Step 2: Classical MD simulation of fracture in Si</a></li>
<li class="toctree-l3"><a class="reference internal" href="adaptive-qmmm-step3.html">Step 3: LOTF hybrid MD simulation of fracture in Si</a></li>
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<div class="section" id="adaptive-qm-mm-md-of-fracture-in-silicon">
<span id="qmmm-tutorial"></span><h1>Adaptive QM/MM MD of Fracture in Silicon<a class="headerlink" href="#adaptive-qm-mm-md-of-fracture-in-silicon" title="Permalink to this headline">¶</a></h1>
<p>This tutorial has been prepared for use at a hands-on session at the
<a class="reference external" href="http://www.adglass.eu/adglass_news.html">ADGLASS Winter School on Advanced Molecular Dynamics Simulations</a>, ICTP, Trieste, February
2013.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
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<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Authors:</th><td class="field-body">James Kermode and Gianpietro Moras</td>
</tr>
<tr class="field-even field"><th class="field-name">Date:</th><td class="field-body">February 2013</td>
</tr>
</tbody>
</table>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="adaptive-qmmm-step0.html">Introduction</a><ul>
<li class="toctree-l2"><a class="reference internal" href="adaptive-qmmm-step0.html#scope-of-the-tutorial">Scope of the tutorial</a></li>
<li class="toctree-l2"><a class="reference internal" href="adaptive-qmmm-step0.html#practical-considerations">Practical considerations</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="adaptive-qmmm-theory.html">Theoretical background</a><ul>
<li class="toctree-l2"><a class="reference internal" href="adaptive-qmmm-theory.html#introduction-to-atomic-scale-modelling-of-fracture">Introduction to Atomic-scale Modelling of Fracture</a></li>
<li class="toctree-l2"><a class="reference internal" href="adaptive-qmmm-theory.html#classical-interatomic-potentials-for-silicon">Classical interatomic potentials for silicon</a></li>
<li class="toctree-l2"><a class="reference internal" href="adaptive-qmmm-theory.html#qm-mm-force-mixing-and-the-learn-on-the-fly-scheme">QM/MM Force Mixing and the ‘Learn on the Fly’ scheme</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="adaptive-qmmm-step1.html">Step 1: Setup of the Silicon model system</a><ul>
<li class="toctree-l2"><a class="reference internal" href="adaptive-qmmm-step1.html#building-the-bulk-unit-cell-30-minutes">1.1 Building the bulk unit cell (30 minutes)</a></li>
<li class="toctree-l2"><a class="reference internal" href="adaptive-qmmm-step1.html#calculation-of-elastic-and-surface-properties-of-silicon-30-minutes">1.2 Calculation of elastic and surface properties of silicon (30 minutes)</a></li>
<li class="toctree-l2"><a class="reference internal" href="adaptive-qmmm-step1.html#setup-of-the-crack-slab-supercell-30-minutes">1.3 Setup of the crack slab supercell (30 minutes)</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="adaptive-qmmm-step2.html">Step 2: Classical MD simulation of fracture in Si</a><ul>
<li class="toctree-l2"><a class="reference internal" href="adaptive-qmmm-step2.html#initialisation-of-the-atomic-system-20-minutes">2.1 Initialisation of the atomic system (20 minutes)</a></li>
<li class="toctree-l2"><a class="reference internal" href="adaptive-qmmm-step2.html#setup-and-run-the-classical-md-20-minutes">2.2 Setup and run the classical MD (20 minutes)</a></li>
<li class="toctree-l2"><a class="reference internal" href="adaptive-qmmm-step2.html#visualisation-and-analysis-as-time-permits">2.3 Visualisation and Analysis (as time permits)</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="adaptive-qmmm-step3.html">Step 3: LOTF hybrid MD simulation of fracture in Si</a><ul>
<li class="toctree-l2"><a class="reference internal" href="adaptive-qmmm-step3.html#initialisation-of-the-qm-mm-atomic-system-20-minutes">3.1 Initialisation of the QM/MM atomic system (20 minutes)</a></li>
<li class="toctree-l2"><a class="reference internal" href="adaptive-qmmm-step3.html#setup-and-run-the-adaptive-qm-mm-md-20-minutes">3.2 Setup and run the adaptive QM/MM MD (20 minutes)</a></li>
<li class="toctree-l2"><a class="reference internal" href="adaptive-qmmm-step3.html#visualisation-and-analysis-as-time-permits">3.3 Visualisation and Analysis (as time permits)</a></li>
<li class="toctree-l2"><a class="reference internal" href="adaptive-qmmm-step3.html#checking-the-predictor-corrector-force-errors-optional">3.4 Checking the predictor/corrector force errors (optional)</a></li>
<li class="toctree-l2"><a class="reference internal" href="adaptive-qmmm-step3.html#further-extension-tasks">Further extension tasks</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="adaptive-qmmm-solutions.html">Solutions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="adaptive-qmmm-solutions.html#step-1-solution-make-crack-py">Step 1 solution — <code class="docutils literal notranslate"><span class="pre">make_crack.py</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="adaptive-qmmm-solutions.html#step-2-solution-run-crack-classical-py">Step 2 solution — <code class="docutils literal notranslate"><span class="pre">run_crack_classical.py</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="adaptive-qmmm-solutions.html#step-3-solution-run-crack-lotf-py">Step 3 solution — <code class="docutils literal notranslate"><span class="pre">run_crack_lotf.py</span></code></a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="adaptive-qmmm-references.html">References</a></li>
</ul>
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